Build the right alignment command for your DNA or RNA-seq data
| Tool | Citation |
|---|---|
| BWA-MEM2 | Vasimuddin M, Misra S, Li H, Aluru S. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. IEEE IPDPS, 2019. doi:10.1109/IPDPS.2019.00041 |
| BWA-MEM | Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997, 2013. arxiv:1303.3997 |
| Bowtie2 | Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nature Methods 9, 357–359, 2012. doi:10.1038/nmeth.1923 |
| Minimap2 | Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34(18):3094–3100, 2018. doi:10.1093/bioinformatics/bty191 |
| STAR | Dobin A, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29(1):15–21, 2013. doi:10.1093/bioinformatics/bts635 |
| HISAT2 | Kim D, et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature Biotechnology 37, 907–915, 2019. doi:10.1038/s41587-019-0201-4 |
| Salmon | Patro R, et al. Salmon provides fast and bias-aware quantification of transcript expression. Nature Methods 14, 417–419, 2017. doi:10.1038/nmeth.4197 |
| Kallisto | Bray NL, et al. Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology 34, 525–527, 2016. doi:10.1038/nbt.3519 |
| samtools | Danecek P, et al. Twelve years of SAMtools and BCFtools. GigaScience 10(2):giab008, 2021. doi:10.1093/gigascience/giab008 |
| vg / vg giraffe | Sirén J, et al. Pangenomics enables genotyping of known structural variants in 5202 diverse genomes. Science 374(6574):abg8871, 2021. doi:10.1126/science.abg8871 |
| GraphAligner | Rautiainen M, Marschall T. GraphAligner: rapid and versatile sequence-to-graph alignment. Genome Biology 21:253, 2020. doi:10.1186/s13059-020-02157-2 |